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| Status |
Public on Sep 19, 2013 |
| Title |
mDip_hmc |
| Sample type |
SRA |
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| Source name |
honey bee
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| Organism |
Apis mellifera |
| Characteristics |
tissue: head
medip antibody: Rabbit polyclonal hmC antibody(Active Motif, Inc.)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
meDIP: Shear DNA to ~600bp fragments: 3µg DNA + TE to 130µl in microTUBE. Denature DNA, 125µl (3µg) sheared DNA + 330µl TE. IP and wash: add 51µl 10x IP buffer + 3µl (1µg/µl) antibody; incubate > 2hours at 4C; add 25µl protein G beads; incubate > 2hours; collect beads with a magnetic rack; wash beads with 700µl 1xIP buffer, incubating 10 minutes x RT x 900rpm (or RT rotator); repeat wash 2 more times. The mC antibodies were mouse monoclonal (Active Motif, Inc.) and the hmC antibodies were rabbit polyclonal (Active Motif, Inc.). Immunoprecipitation was with protein G beads (Active Motif, Inc.) following the manufacturer’s protocol.
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| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
IP hmC antibody
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| Data processing |
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Pvu-Seq reads: Peak detection using MACS v1.4 (forcing zero length shift)
Genome_build: Amel2
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)
Image analysis, base calling and sequence extraction was performed using standard Illumina Pipeline v1.6 software
Read mapping was performed using BWA, except for RNA-Seq which was done by Bowtie (TopHat)
For BS-Seq analysis we used our analysis pipeline (BS-Miner)
RNA-Seq primary analysis was performed using Tophat-Cufflinks suite
For mDip analysis, peak detection was performed using MACS
Genome_build: Amel_2.0
Supplementary_files_format_and_content: Standard VCF (methylation calls), BED files (peaks), FPKM (RNA-seq)
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| Submission date |
Sep 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pablo Cingolani |
| E-mail(s) |
[email protected]
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| Organization name |
McGill University
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| Street address |
701 Avenue du Docteur-Penfield
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| City |
Montréal |
| State/province |
Quebec |
| ZIP/Postal code |
H3A-1A5 |
| Country |
Canada |
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| Platform ID |
GPL9909 |
| Series (1) |
| GSE50990 |
Intronic Non-CG DNA Hydroxymethylation and Alternative mRNA Splicing in Honey Bees |
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| Relations |
| BioSample |
SAMN02358646 |
| SRA |
SRX352961 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1234292_mDip_hmc_peaks.bed.gz |
194.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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